Merge branch 'hotfix/next' v3.1.5

Conflicts:
	CHANGELOG.txt

CHANGELOG.txt

@@ -1,13 +1,32 @@
-3.2
+3.1.5 (2014-10-10)
 ------------------
 
+HEALTH-176: Cannot choose a drug from the dropdown list on Patient->allergies
+HEALTH-174: Unable to add an AR to a Case (missing Client)
+HEALTH-163: Cannot be chosen Immunisation items from dropdown list.
+HEALTH-162: Cannot choose Drug Prohibition Explanation
+HEALTH-169: Analyst can't see Samples site, Admin can.
+HEALTH-168: Diagnosis ICD widget does not complete from Code, Description
+HEALTH-161: In Add Patient, after introducing the Birth Date, the patient's age don't get filled automatically.
+HEALTH-157: Patient field is missing in AR add views
+HEALTH-150: Compatibility with the new JS loader machinery
+HEALTH-164: Editing a patient, location not have to be important on Travel History field
+HEALTH-166: "Patient Age at Case Onset Date" in Add Case cannot be filled
+HEALTH-172: Anything is displayed on drugs list
+HEALTH-173: ImmunizationHistory cannot save data
+HEALTH-149: Compatibility with the new Bika LIMS reporting subsystem
+HEALTH-152: Upgrade the test data worksheet
 HEALTH-145: Health icons not used. And 1 more
+HEALTH-152: Upgrade the test data worksheet
+
+- Plus Bika-LIMS 3.1.5: http://git.io/ogjDuQ
 
 
 3.1.2.1 (2014-08-05)
 ------------------
 
 HEALTH-144: Set up data: Identifier Types NameError: global name '_id' is not defined
+HEALTH-143: Can not create site
 
 
 3.1.2 (2014-07-25)

README.md

@@ -1,16 +1,27 @@
-Bika Health 3.1.2 (Naringenin)
-================
+Bika Health 3.1.5 (Naringenin)
+==============================
 
 Bika Laboratory Information Management System customised for use in Health laboratories.
 
 [Naringenin](http://en.wikipedia.org/wiki/Naringenin) is a flavanone, a typeof flavonoid, that is considered to have a bioactive effect on human health as antioxidant, free radical scavenger, anti-inflammatory, carbohydrate metabolism promoter, and immune system modulator. It is the predominant flavanone in grapefruit.
 
-Installation instructions:
+Installation and upgrades
+-------------------------
+Bika Health can be installed on Windows, Mac OS X, Linux, BSD and other platforms:
+https://github.com/bikalabs/bika.health/wiki/Installing-Bika-Health-Extension
 
-1. Read https://plone.org/documentation/manual/installing-plone
-2. Read https://plone.org/documentation/kb/installing-add-ons-quick-how-to
-3. Install Plone and the "bika.health" package
+You might also find useful the following recipes:
+- Installing Bika LIMS: https://github.com/bikalabs/Bika-LIMS/wiki/Bika-LIMS-Installation
+- Installing Plone: https://plone.org/documentation/manual/installing-plone
+- Installing Plone add-ons: https://plone.org/documentation/kb/installing-add-ons-quick-how-to
 
+Documentation
+-------------
+- Bika LIMS User Manual: http://demo.bikalabs.com/knowledge-centre/manual/bika-3-user-manual
+- Bika LIMS Wiki: http://github.com/bikalabs/Bika-LIMS/wiki
+
+Feedback and support
+--------------------
 If you have questions, please post to one of our mailing lists:
 
 * Bika Health Users: http://groups.google.com/forum/?hl=en#!forum/bika-health
@@ -19,13 +30,3 @@ If you have questions, please post to one of our mailing lists:
 * Developers: http://lists.sourceforge.net/lists/listinfo/bika-developers
 
 Please log issues, feature requests, or bug reports in the [issue tracker](http://jira.bikalabs.com/)
-
-
-
-Bika Lab Systems
-info@bikalabs.com
-http://www.bikalabs.com
-
-Naralabs
-info@naralabs.com
-http://www.naralabs.com

bika/health/adapters/configure.zcml

@@ -0,0 +1,14 @@
+<configure
+    xmlns="http://namespaces.zope.org/zope"
+    xmlns:browser="http://namespaces.zope.org/browser"
+    xmlns:i18n="http://namespaces.zope.org/i18n"
+    i18n_domain="bika">
+
+    <adapter
+      factory=".widgetvisibility.PatientFieldsWidgetVisibility"
+      provides="bika.lims.interfaces.IATWidgetVisibility"
+      for="bika.lims.interfaces.IAnalysisRequest"
+      name="PatientFieldsWidgetVisibility"
+    />
+
+</configure>

bika/health/adapters/widgetvisibility.py

@@ -0,0 +1,53 @@
+# -*- coding:utf-8 -*-
+from Products.CMFCore.WorkflowCore import WorkflowException
+from bika.lims.utils import getHiddenAttributesForClass
+from types import DictType
+from Products.CMFCore.utils import getToolByName
+from bika.lims.interfaces import IATWidgetVisibility
+from zope.interface import implements
+from bika.health.permissions import ViewPatients
+
+_marker = []
+
+
+class PatientFieldsWidgetVisibility(object):
+    """This will force readonly fields to be uneditable, and viewable only by
+     those with ViewPatients permission.
+    """
+    implements(IATWidgetVisibility)
+
+    def __init__(self, context):
+        self.context = context
+        # self.sort = 100
+
+    def __call__(self, context, mode, field, default):
+        state = default if default else 'invisible'
+
+        header_table_fields = ['Patient',
+                               'PatientID',
+                               'ClientPatientID']
+        readonly_fields = ['Batch',
+                           'Patient',
+                           'PatientID',
+                           'ClientPatientID']
+
+        mtool = getToolByName(self.context, 'portal_membership')
+        has_perm = mtool.checkPermission(ViewPatients, self.context)
+
+        fieldName = field.getName()
+        if fieldName not in header_table_fields and fieldName not in readonly_fields:
+            return state
+
+        #from bika.lims import logger
+        #oldstate = state
+        if has_perm:
+           if mode == 'header_table' and fieldName in header_table_fields:
+               state = 'visible'
+           if mode == 'view' and fieldName in readonly_fields:
+               state = 'visible'
+        if mode == 'edit' and fieldName in readonly_fields:
+               state = 'invisible'
+        #if state != oldstate:
+        #    logger.info("PatientFieldsWidgetVisibility %s %s %s %s->%s"%(self.context, has_perm, fieldName, oldstate, state))
+
+        return state

bika/health/browser/analysisrequest/overrides.zcml

@@ -4,17 +4,10 @@
            xmlns:browser="http://namespaces.zope.org/browser"
            xmlns:five="http://namespaces.zope.org/five">
 
-    <adapter
-      factory="bika.health.browser.analysisrequest.widgets.WidgetVisibility"
-      provides="bika.lims.interfaces.IWidgetVisibility"
-      for="bika.lims.interfaces.IAnalysisRequest"
-      name="getWidgetVisibility"
-    />
-
     <browser:page
       for="bika.lims.interfaces.IAnalysisRequest"
       name="workflow_action"
-      class="bika.health.browser.analysisrequest.workflow.WorkflowAction"
+      class="bika.health.browser.analysisrequest.workflow.AnalysisRequestWorkflowAction"
       permission="zope.Public"
       layer="bika.lims.interfaces.IBikaLIMS"
     />
@@ -43,4 +36,21 @@
       layer="bika.lims.interfaces.IBikaLIMS"
     />
 
+    <browser:page
+      for="bika.lims.interfaces.IAnalysisRequest"
+      name="publish"
+      class="bika.health.browser.analysisrequest.publish.AnalysisRequestPublishView"
+      permission="bika.lims.ManageAnalysisRequests"
+      layer="bika.lims.interfaces.IBikaLIMS"
+    />
+
+    <!-- Multiple analysis requests results preview -->
+    <browser:page
+      for="bika.lims.interfaces.IAnalysisRequestsFolder"
+      name="publish"
+      class="bika.health.browser.analysisrequest.publish.AnalysisRequestPublishView"
+      permission="bika.lims.ManageAnalysisRequests"
+      layer="bika.lims.interfaces.IBikaLIMS"
+    />
+
 </configure>

bika/health/browser/analysisrequest/publish.py

@@ -1,15 +1,83 @@
-from bika.lims.browser.publish import doPublish
+from bika.lims.browser.analysisrequest.publish import \
+    AnalysisRequestPublishView as _AnalysisRequestPublishView
 from bika.health import bikaMessageFactory as _h
 from bika.lims import bikaMessageFactory as _
 from Products.Five.browser.pagetemplatefile import ViewPageTemplateFile
+import glob, os, sys, traceback
 
-
-class AnalysisRequestPublish(doPublish):
-
-    template = ViewPageTemplateFile("report_results.pt")
+class AnalysisRequestPublishView(_AnalysisRequestPublishView):
 
     def __call__(self):
-        return super(AnalysisRequestPublish, self).__call__()
+        return super(AnalysisRequestPublishView, self).__call__()
+
+    def getAvailableFormats(self):
+        """ Overrides
+            Looks for templates inside bika.health's templates/reports
+            folder, as well as bika.lims's templates/reports directory
+        """
+        # bika.lims templates
+        btempl = _AnalysisRequestPublishView.getAvailableFormats(self)
+        for tmpl in btempl:
+            tmpl['title'] = '%s: %s' % ('bika.lims', tmpl['title']);
+            tmpl['id'] = '%s:%s' % ('bika.lims', tmpl['id']);
+
+        # bika.health templates
+        tempath = self._getTemplatesResourcePath('*.pt')
+        templates = [t.split('/')[-1] for t in glob.glob(tempath)]
+        out = []
+        for template in templates:
+            out.append({
+                'id': '%s:%s' % ('bika.health', template),
+                'title': '%s: %s' % ('bika.health', template[:-3])})
+
+        out.extend(btempl)
+        return out
+
+    def getReportTemplate(self):
+        """ Overrides
+            Returns the template for the current ar and moves to the
+            next ar to be processed. Uses the selected template
+            specified in the request ('template' parameter)
+        """
+        embedt = self.request.get('template', self._DEFAULT_TEMPLATE)
+        path = self._getTemplatesResourcePath(embedt)
+        embed = ViewPageTemplateFile(path)
+        reptemplate = ""
+        try:
+            reptemplate = embed(self)
+        except:
+            tbex = traceback.format_exc()
+            arid = self._ars[self._current_ar_index].id
+            reptemplate = "<div class='error-report'>%s - %s '%s':<pre>%s</pre></div>" % (arid, _("Unable to load the template"), embedt, tbex)
+            self.logger.error(tbex);
+        self._nextAnalysisRequest()
+        return reptemplate
+
+    def getReportStyle(self):
+        """ Overrides
+            Returns the CSS to be used in the current template
+        """
+        embedt = self.request.get('template', self._DEFAULT_TEMPLATE)
+        path = "%s.css" % self._getTemplatesResourcePath(embedt)[:-3]
+        content = ''
+        with open(path, 'r') as content_file:
+            content = content_file.read()
+        return content
+
+    def _getTemplatesResourcePath(self, resource):
+        """ Returns the full path from any resource located inside
+            /templates/reports, either from inside bika.lims project
+            or bika.health project
+        """
+        this_dir = os.path.dirname(os.path.abspath(__file__))
+        res = resource
+        if 'bika.lims:' in resource:
+            this_dir = str.replace(this_dir, "bika.health/bika/health", "bika.lims/bika/lims")
+            res = str.replace(resource, 'bika.lims:', '')
+        res = str.replace(res, 'bika.health:', '')
+        path = os.path.join(this_dir, 'templates/reports')
+        path = '%s/%s' % (path, res)
+        return path
 
     def get_patient(self, ar):
         return ar.Schema().getField('Patient').get(ar) \
@@ -46,9 +114,9 @@ def get_formatted_lab_address(self):
             addr = self.get_formatted_address(client_address)
         return addr
 
-    def get_formatted_client_address(self):
-        client = self.ar['obj'].getClient()
-        contact = self.ar['obj'].getContact();
+    def get_formatted_client_address(self, ar):
+        client = ar.getClient()
+        contact = ar.getContact();
         client_address = client.getPostalAddress() \
             or contact.getBillingAddress() \
             or contact.getPhysicalAddress()